Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012431.1 Corchorus capsularis cultivar CVL-1 contig12452, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 59297
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1181 original size:322 final size:320
Alignment explanation
Indices: 1--1682 Score: 2391
Period size: 322 Copynumber: 5.3 Consensus size: 320
* ** *
1 TTTTCCTTAATTTTTGCCACAATACTCTGAAAAATTAAATAATTCAACACTGAAAAGATTGCAGG
1 TTTTTCTTAATTTTTGCCACAATACTCTGAAAAATTAAATAATTCAACACCAAAAAGATTGAAGG
* * *
66 GTTTTTCACGCTTCTGATATCG--------TTTTTTCCATTTTTTTTCTAATTAAATCGACACAA
66 GTTTTTCACGCTTCTGATATCGTTTTCCATTTTTTTCCAATTTATTTCTAATTAAATCGAAACAA
* * * *
123 GATTTAGATGCTTGTAAAAACAAATCTTTAATTCCATTGTGGCTAAGAATTAATTAGATGGATAT
131 GATTCAGATGCTTGTAAAAACAAATCCTTAATTCCATTGTGGCTAAGATTTAATTAGATGAATAT
*
188 AGATATTTCGAGGAGTATTTAAACCAAAAATCATGCAAAACTGAGTCGGGTCCCCGAAACGCATT
196 AGATATTTCGAGGAGTATTTAAACCAAAAATCATGCAAAACTGAGTCGGGGCCCCGAAACGCATT
* *
253 TTAAGGCAAAAACCGTGATGGTTAGTCCACGATTTCGGTTAAAAACTTACCCG-AAA-TT
261 TTAAGGCAAAAACCGTGATGGTTAGTCCACGATTTCGGCTAAAAACTGACCCGAAAATTT
* * *
311 TTTTT-TTAATTTTTGCCACAATACTCTAAAAAATTAATTAATTCAACACCAAAAAGATTGCAGG
1 TTTTTCTTAATTTTTGCCACAATACTCTGAAAAATTAAATAATTCAACACCAAAAAGATTGAAGG
* *
375 G-ATTTCACACTTCTGATATCGTTTTTCCATTTTTTTCCGAATTTATTTCTAA-T---T----AC
66 GTTTTTCACGCTTCTGATATCG-TTTTCCATTTTTTTCC-AATTTATTTCTAATTAAATCGAAAC
* **
431 AAGATTCAGATGCTTGTAAAAACAAATTCTTAATTCCATTGTGGCTAAGATTTGGTTAGATGAAT
129 AAGATTCAGATGCTTGTAAAAACAAATCCTTAATTCCATTGTGGCTAAGATTTAATTAGATGAAT
* * * * * * *
496 ATAGATATTCCAAGGAGTATTTAAACAAAAAATCAGGCAAAATTGAGCCGGTGCCCCGAAACGCA
194 ATAGATATTTCGAGGAGTATTTAAACCAAAAATCATGCAAAACTGAGTCGGGGCCCCGAAACGCA
** **
561 TTTTAAAGAAAAAAAACTTTGATGGTTAGTCCACGATTTCGGCTAAAAACTGACCCGAAAATTT
259 TTTT-AAG-GCAAAAACCGTGATGGTTAGTCCACGATTTCGGCTAAAAACTGACCCGAAAATTT
* * *
625 TTTTTCTTAATCTTTT-CCACAATATTCTGAAAAATTAAATAATTCAACACCGAAAAGATTTAAG
1 TTTTTCTTAAT-TTTTGCCACAATACTCTGAAAAATTAAATAATTCAACACCAAAAAGATTGAAG
* * *
689 GGTTTCTCACGTTTCTGATATCGTTTTCCA-TTTTTTCTGAATTTATTTCTAATTAAATTCGAAA
65 GGTTTTTCACGCTTCTGATATCGTTTTCCATTTTTTTC-CAATTTATTTCTAATTAAA-TCGAAA
* * *
753 CAAGATTCAGATGCTTGTAAAAAGAAATCCTTAATTTCATTATGGCTAAGATTTAATTAGATGAA
128 CAAGATTCAGATGCTTGTAAAAACAAATCCTTAATTCCATTGTGGCTAAGATTTAATTAGATGAA
* * * *
818 TATAGATATTTCGAGGAGTATTTAAACCAAAACTTATGCAAAACTCAGCCGGGGCCCCGAAACGC
193 TATAGATATTTCGAGGAGTATTTAAACCAAAAATCATGCAAAACTGAGTCGGGGCCCCGAAACGC
**
883 ATTTTAAGGCAAAAACCGTGATGGTTAGTCCACGATTTCTCCTAAAAACTGACCCGAAAATTT
258 ATTTTAAGGCAAAAACCGTGATGGTTAGTCCACGATTTCGGCTAAAAACTGACCCGAAAATTT
* * * *
946 TTTTTCTTAATTTTTGCCACAATGCTCTGAAAAAATAAATAATTCAACACCAAAAAGATTGTATG
1 TTTTTCTTAATTTTTGCCACAATACTCTGAAAAATTAAATAATTCAACACCAAAAAGATTGAAGG
1011 GTTTTTCACGCTTCTGATATCGTTTTTCCATTTTTTTCCATATTTATTTCTAATTAAATCGAAAC
66 GTTTTTCACGCTTCTGATATCG-TTTTCCATTTTTTTCCA-ATTTATTTCTAATTAAATCGAAAC
* * *
1076 AAGATTTAGATGCTTGTAAAAACAAATCCTTAATTCCATTGTGGCTAAGATTTAATAAGATGGAT
129 AAGATTCAGATGCTTGTAAAAACAAATCCTTAATTCCATTGTGGCTAAGATTTAATTAGATGAAT
*
1141 ATAGATATTTCGAGGAGTATTTAAACCAAAAATCATGCAAAACTGAGTCGGGTCCCCGAAACGCA
194 ATAGATATTTCGAGGAGTATTTAAACCAAAAATCATGCAAAACTGAGTCGGGGCCCCGAAACGCA
* * *
1206 TTTTAAGGCAAAAACCGTGATGGTTAGTCCACAATTTTCGGCTAAAAACTGACTCGAAAAATT
259 TTTTAAGGCAAAAACCGTGATGGTTAGTCCACGA-TTTCGGCTAAAAACTGACCCGAAAATTT
* * * *
1269 TTTTTCTTAAATTTCGCCACAATATTCTGAAAATTTAAATAATTCAACACCAAAAAGATTGAAGG
1 TTTTTCTTAATTTTTGCCACAATACTCTGAAAAATTAAATAATTCAACACCAAAAAGATTGAAGG
** *
1334 GTTTTTCACATTTTTGATATCGTTTTCCATTTTTTTCCGAATTTATTTCTAATTAAATCGAAACA
66 GTTTTTCACGCTTCTGATATCGTTTTCCATTTTTTTCC-AATTTATTTCTAATTAAATCGAAACA
**
1399 AGATTCAGATGCTTGTAAAAACAAATCCTTAATTCCATTGTGGCTAAGATTTGGTTAGATGAATA
130 AGATTCAGATGCTTGTAAAAACAAATCCTTAATTCCATTGTGGCTAAGATTTAATTAGATGAATA
* *
1464 TAGATATTTCGAGGAGTATTTAAACCAAAAATCATGCAAAACTGAGTCGGTGCCCCGAAAGGCAT
195 TAGATATTTCGAGGAGTATTTAAACCAAAAATCATGCAAAACTGAGTCGGGGCCCCGAAACGCAT
* *
1529 TTTAAGGCAAAAAACCGTGATGGTTAGTCCACGATTTCGGTTAAAAACTGACCCAAAATATTT
260 TTTAAGGC-AAAAACCGTGATGGTTAGTCCACGATTTCGGCTAAAAACTGACCCGAAA-ATTT
* * *
1592 TTTTTCTTAATTTTTGCCACACTACTCTGAAAAATTAAATAATTCAATACCAAAATGATTGAAGG
1 TTTTTCTTAATTTTTGCCACAATACTCTGAAAAATTAAATAATTCAACACCAAAAAGATTGAAGG
* * *
1657 GCTTTTCACGCTTATAATATCGTTTT
66 GTTTTTCACGCTTCTGATATCGTTTT
1683 GCCACAATAC
Statistics
Matches: 1213, Mismatches: 124, Indels: 57
0.87 0.09 0.04
Matches are distributed among these distances:
308 18 0.01
309 56 0.05
310 125 0.10
311 3 0.00
312 42 0.03
313 3 0.00
314 28 0.02
315 57 0.05
316 20 0.02
317 9 0.01
318 11 0.01
319 1 0.00
320 4 0.00
321 122 0.10
322 362 0.30
323 352 0.29
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.34
Consensus pattern (320 bp):
TTTTTCTTAATTTTTGCCACAATACTCTGAAAAATTAAATAATTCAACACCAAAAAGATTGAAGG
GTTTTTCACGCTTCTGATATCGTTTTCCATTTTTTTCCAATTTATTTCTAATTAAATCGAAACAA
GATTCAGATGCTTGTAAAAACAAATCCTTAATTCCATTGTGGCTAAGATTTAATTAGATGAATAT
AGATATTTCGAGGAGTATTTAAACCAAAAATCATGCAAAACTGAGTCGGGGCCCCGAAACGCATT
TTAAGGCAAAAACCGTGATGGTTAGTCCACGATTTCGGCTAAAAACTGACCCGAAAATTT
Found at i:2042 original size:18 final size:19
Alignment explanation
Indices: 2000--2042 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1990 CATAATTAAT
*
2000 AAAAAAGTTGAATCATCTA
1 AAAAAAGTTAAATCATCTA
*
2019 AAAAAAGTTAAATGA-CTA
1 AAAAAAGTTAAATCATCTA
2037 AAAAAA
1 AAAAAA
2043 TACTTATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.63, C:0.07, G:0.09, T:0.21
Consensus pattern (19 bp):
AAAAAAGTTAAATCATCTA
Found at i:5795 original size:4 final size:4
Alignment explanation
Indices: 5786--5825 Score: 80
Period size: 4 Copynumber: 10.0 Consensus size: 4
5776 TTAAGAATAT
5786 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
5826 AGCATGAGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:7685 original size:31 final size:31
Alignment explanation
Indices: 7645--7708 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
7635 ACAATCATCA
7645 ATAACCAAAAGGAAAATGTCAAAATAATAAT
1 ATAACCAAAAGGAAAATGTCAAAATAATAAT
*
7676 ATAATCAAAAGGAAAATGTCAAAATAATAAT
1 ATAACCAAAAGGAAAATGTCAAAATAATAAT
7707 AT
1 AT
7709 TAATAACTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.61, C:0.08, G:0.09, T:0.22
Consensus pattern (31 bp):
ATAACCAAAAGGAAAATGTCAAAATAATAAT
Found at i:10478 original size:22 final size:22
Alignment explanation
Indices: 10450--10497 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
10440 TCACGAAGCC
10450 AGCTTAAGAAACAAACAAGATG
1 AGCTTAAGAAACAAACAAGATG
10472 AGCTTAAGAAACAAACAAGATG
1 AGCTTAAGAAACAAACAAGATG
10494 AGCT
1 AGCT
10498 CAGATACAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.52, C:0.15, G:0.19, T:0.15
Consensus pattern (22 bp):
AGCTTAAGAAACAAACAAGATG
Found at i:21823 original size:26 final size:26
Alignment explanation
Indices: 21794--21875 Score: 66
Period size: 26 Copynumber: 3.2 Consensus size: 26
21784 TGTCATTTAC
21794 CTTAATTAAATTTGTTTCATCAATGG
1 CTTAATTAAATTTGTTTCATCAATGG
* **
21820 CTTAA--AAAGTTTTTAGTTT-AT--TTAC
1 CTTAATTAAA---TTT-GTTTCATCAATGG
21845 CTTAATTAAATTTGTTTCATCAATGG
1 CTTAATTAAATTTGTTTCATCAATGG
21871 CTTAA
1 CTTAA
21876 AAAGTTTTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 18
0.63 0.09 0.28
Matches are distributed among these distances:
23 4 0.10
24 8 0.20
25 6 0.15
26 11 0.27
27 8 0.20
28 4 0.10
ACGTcount: A:0.32, C:0.11, G:0.10, T:0.48
Consensus pattern (26 bp):
CTTAATTAAATTTGTTTCATCAATGG
Found at i:21843 original size:51 final size:52
Alignment explanation
Indices: 21786--21894 Score: 211
Period size: 51 Copynumber: 2.1 Consensus size: 52
21776 CTCCATATTG
21786 TCATTTACCTTAATTAAATTTGTTTCATCAATGGCTTAAAAAGTTTTTAGTT
1 TCATTTACCTTAATTAAATTTGTTTCATCAATGGCTTAAAAAGTTTTTAGTT
21838 T-ATTTACCTTAATTAAATTTGTTTCATCAATGGCTTAAAAAGTTTTTAGTT
1 TCATTTACCTTAATTAAATTTGTTTCATCAATGGCTTAAAAAGTTTTTAGTT
21889 TCATTT
1 TCATTT
21895 TCTAACTGCT
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
51 51 0.91
52 5 0.09
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.50
Consensus pattern (52 bp):
TCATTTACCTTAATTAAATTTGTTTCATCAATGGCTTAAAAAGTTTTTAGTT
Found at i:22491 original size:32 final size:32
Alignment explanation
Indices: 22455--22518 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
22445 GGTAGCATGG
*
22455 AGTTTTTTCTGCTCGAGTTGATCTAAATCACT
1 AGTTTTTTCTACTCGAGTTGATCTAAATCACT
22487 AGTTTTTTCTACTCGAGTTGATCTAAATCACT
1 AGTTTTTTCTACTCGAGTTGATCTAAATCACT
22519 TAATATCTAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.23, C:0.19, G:0.14, T:0.44
Consensus pattern (32 bp):
AGTTTTTTCTACTCGAGTTGATCTAAATCACT
Found at i:31264 original size:17 final size:17
Alignment explanation
Indices: 31218--31270 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
31208 AACCCATGTA
* *
31218 ATCTTTGATCACCGGTG
1 ATCTTAGATCACTGGTG
*
31235 ATCTTACATCACTGGTG
1 ATCTTAGATCACTGGTG
*
31252 ATCTTAGATCACTAGTG
1 ATCTTAGATCACTGGTG
31269 AT
1 AT
31271 TTGGGGGTGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.36
Consensus pattern (17 bp):
ATCTTAGATCACTGGTG
Found at i:33696 original size:30 final size:31
Alignment explanation
Indices: 33634--33708 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 31
33624 AAATTTGGTG
*
33634 AGGGACCCAATTGCTCAATTAACTCAACTTC
1 AGGGACCCAATTGCTCAACTAACTCAACTTC
* *
33665 AGGGACTCAATTGCTC-ACTAAGTTC-ACTTC
1 AGGGACCCAATTGCTCAACTAA-CTCAACTTC
*
33695 AGGGACCCATTTGC
1 AGGGACCCAATTGC
33709 ACATTTGCCC
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
30 21 0.55
31 17 0.45
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (31 bp):
AGGGACCCAATTGCTCAACTAACTCAACTTC
Found at i:34756 original size:29 final size:29
Alignment explanation
Indices: 34705--34785 Score: 85
Period size: 29 Copynumber: 2.7 Consensus size: 29
34695 GCTCAGTCAA
* * *
34705 CTCCACTTCAGGGACTAAATTGCATAT-TT
1 CTCCACTTGAGGGACCAATTTGC-TATGTT
34734 -TCACACTTGAGGGACCAATTTGCTATGTT
1 CTC-CACTTGAGGGACCAATTTGCTATGTT
34763 CGCTCCACTTGAGGGACCAATTT
1 --CTCCACTTGAGGGACCAATTT
34786 TGTACTTTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
28 5 0.11
29 19 0.43
31 18 0.41
32 2 0.05
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.32
Consensus pattern (29 bp):
CTCCACTTGAGGGACCAATTTGCTATGTT
Found at i:36315 original size:11 final size:11
Alignment explanation
Indices: 36272--36309 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
36262 TTCCTATATA
*
36272 AAATAAATTAT
1 AAATTAATTAT
36283 CAAA-TAATTAT
1 -AAATTAATTAT
36294 AAATTAATTAT
1 AAATTAATTAT
36305 AAATT
1 AAATT
36310 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:39821 original size:22 final size:21
Alignment explanation
Indices: 39781--39826 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
39771 TATCGTTGTT
* **
39781 TTTGATTTCTTGATTTTCTGTA
1 TTTGATTTATTGACATTCTG-A
39803 TTTGATTTATTGACATTCTGA
1 TTTGATTTATTGACATTCTGA
39824 TTT
1 TTT
39827 TCAAGAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.17, C:0.09, G:0.13, T:0.61
Consensus pattern (21 bp):
TTTGATTTATTGACATTCTGA
Found at i:47606 original size:2 final size:2
Alignment explanation
Indices: 47599--47634 Score: 54
Period size: 2 Copynumber: 17.5 Consensus size: 2
47589 CTAAAAGGGA
*
47599 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT GAT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT A
47635 CTTTTAACAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48881 original size:31 final size:29
Alignment explanation
Indices: 48808--48881 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
48798 ACGTGATATG
* *
48808 TGGCATGCCATGTGTACCAAAAAGCGACG
1 TGGCATGCCACGTGTACCAAAAAGCGACA
* * *
48837 TGTCACGCCACGTGTACCAAAAAGTGACACA
1 TGGCATGCCACGTGTACCAAAAAGCG--ACA
48868 TGGCATGCCACGTG
1 TGGCATGCCACGTG
48882 CCACTTTTTT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
29 22 0.61
31 14 0.39
ACGTcount: A:0.30, C:0.27, G:0.26, T:0.18
Consensus pattern (29 bp):
TGGCATGCCACGTGTACCAAAAAGCGACA
Found at i:51039 original size:43 final size:43
Alignment explanation
Indices: 50990--51075 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
50980 GATGGTTAGG
50990 TAATAGTACTACTACTGGAAAAAATGTCTTTTGCGATGTTTAT
1 TAATAGTACTACTACTGGAAAAAATGTCTTTTGCGATGTTTAT
51033 TAATAGTACTACTACTGGAAAAAATGTCTTTTGCGATGTTTAT
1 TAATAGTACTACTACTGGAAAAAATGTCTTTTGCGATGTTTAT
51076 AAATCGGTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.40
Consensus pattern (43 bp):
TAATAGTACTACTACTGGAAAAAATGTCTTTTGCGATGTTTAT
Done.